Hostname: page-component-78c5997874-94fs2 Total loading time: 0 Render date: 2024-11-10T07:29:52.974Z Has data issue: false hasContentIssue false
  • English
  • Français

DNA Microarrays for Polymorphism Detection and Genotyping: Utility in the Understanding of Complex Neuropsychiatric Diseases

Published online by Cambridge University Press:  07 November 2014

Pamela Sklar ,
David Altshuler ,
Michele Cargill  and
Joel N. Hirschhorn
Get access Rights & Permissions [Opens in a new window]

Abstract

As the Human Genome Project completes the first human genome sequence, attention has turned to how this information can be used to understand disease. The availability of sequences for all genes will allow a comprehensive evaluation of each gene's contribution to disease. Approaches involving collecting specific gene variants and monitoring expression levels using DNA microarrays facilitate collecting information about DNA and RNA in a rapid and highly parallel manner. Developing an extensive catalogue of polymorphisms will become increasingly important in the context of studies of complex genetic diseases such as schizophrenia and bipolar disorder.

Type
Feature Articles
Information
CNS Spectrums , Volume 4 , Issue 5: Molecular Genetics: Part One , May 1999 , pp. 59 - 74
Copyright
Copyright © Cambridge University Press 1999

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

1.Schena, M, Heller, R, Chai, A, Brown, PO, Davis, RW, et al.Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 1996;93:10614–10619.CrossRefGoogle ScholarPubMed
2.Schena, M, Shalon, D, Davis, RW, Brown, PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray [see comments]. Science. 1995;270:467–470.CrossRefGoogle ScholarPubMed
3.Shalon, D, Smith, SJ, Brown, PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996;6:639–645.CrossRefGoogle ScholarPubMed
4.DeRisi, JL, Iyer, VR, Brown, PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997;278:680–686.CrossRefGoogle ScholarPubMed
5.Lashkari, DA, DeRisi, JL, McCusker, JH, et al.Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA. 1997;94:13057–13062.CrossRefGoogle ScholarPubMed
6.Pease, AC, Solas, D, Sullivan, EJ, Cronin, MT, Holmes, CP, Fodor, SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA. 1994;91:5022–5026.CrossRefGoogle ScholarPubMed
7.Lockhart, DJ, Dong, H, Byrne, MC, et al.Expression monitoring by hybridization to high-density oligonucleotide arrays [see comments]. Nat Biotechnol. 1996;14:1675–1680.CrossRefGoogle ScholarPubMed
8.The chipping forecast. Nat Genet. 1999;21:3–60.Google Scholar
9.Gottesman, II. Schizophrenia Genesis: The Origins of Madness. New York, NY: Freeman & Company;1991.Google Scholar
10.Craddock, N, Khodel, V, Van Eerdewegh, P, Reich, T. Mathematical limits of multilocus models: the genetic transmission of bipolar disorder. Am J Hum Genet. 1995;57:690–702.Google ScholarPubMed
11.Prescott, CA, Gottesman, II. Genetically mediated vulnerability to schizophrenia. Psychiatr Clin North Am. 1993;16:245–267.CrossRefGoogle ScholarPubMed
12.Bertelsen, A, Harvald, B, Hauge, M. A Danish twin study of manic-depressive disorders. Br J Psychiatry. 1977;130:330–351.CrossRefGoogle ScholarPubMed
13.Cardno, AG, Marshall, EJ, Coid, B, et al.Heritability estimates for psychotic disorders: the Maudsley twin psychosis series. Arch Gen Psychiatry. 1999;56:162–168.CrossRefGoogle ScholarPubMed
14.Collins, FS. Of needles and haystacks: finding human disease genes by positional cloning. Clin Res. 1991;39:615–623.Google ScholarPubMed
15.The Huntington's Disease Collaborative Research Group. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes [see comments]. Cell. 1993;72:971–983.CrossRefGoogle Scholar
16.Goate, A, Chartier-Harlin, MC, Mullan, M, et al.Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease [see comments]. Nature. 1991;349:704–706.CrossRefGoogle ScholarPubMed
17.St George-Hyslop, P, Haines, J, Rogaev, E, et al.Genetic evidence for a novel familial Alzheimer's disease locus on chromosome 14. Nature Genetics. 1992;2:330–334.CrossRefGoogle ScholarPubMed
18.Schellenberg, GD, Bird, TD, Wijsman, EM, et al.Genetic linkage evidence for a familial Alzheimer's disease locus on chromosome 14. Science. 1992;258:668–671.CrossRefGoogle ScholarPubMed
19.Van Broeckhoven, C, Backhovens, H, Cruts, M, et al.Mapping of a gene predisposing to early-onset Alzheimer's disease to chromosome 14q24.3. Nature Genetics. 1992;2:335–339.CrossRefGoogle ScholarPubMed
20.Levy-Lahad, E. Candidate gene for the chromosome 1 familial Alzheimer's disease locus [see comments]. Science. 1995;269:973–977.CrossRefGoogle ScholarPubMed
21.Cruts, M, Hendriks, L, Van Broeckhoven, C. The prese-nilin genes: a new gene family involved in Alzheimer disease pathology. Hum Mol Genet. 1996;5:1449–1455.CrossRefGoogle Scholar
22.Tanzi, RE, Kovacs, DM, Kim, TW, Moir, RD, Guenette, SY, Wasco, W, et al.The gene defects responsible for familial Alzheimer's disease. Neurobiol Dis. 1996;3:159–168.CrossRefGoogle ScholarPubMed
23.Strittmatter, WJ, Saunders, AM, Schmechel, D, et al.Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc Natl Acad Sci USA. 1993;90:1977–1981.CrossRefGoogle ScholarPubMed
24.Corder, EH, Saunders, AM, Strittmatter, WJ, et al.Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families [see comments]. Science. 1993;261:921–923.CrossRefGoogle ScholarPubMed
25.Risch, N, Botstein, D. A manic depressive history [news]. Nat Genet. 1996;12:351–353.CrossRefGoogle ScholarPubMed
26.Moldin, SO. The maddening hunt for madness genes [news]. Nat Genet. 1997;17:127–129.CrossRefGoogle ScholarPubMed
27.Blouin, JL, Dombroski, BA, Nath, SK, et al.Schizophrenia susceptibility loci on chromosomes 13q32 and 8p21. Nat Genet. 1998;20:70–73.CrossRefGoogle ScholarPubMed
28.Risch, N, Merikangas, K. The future of genetic studies of complex human diseases [see comments]. Science. 1996;273:1516–1517.CrossRefGoogle ScholarPubMed
29.Ewens, WJ, Spielman, RS. The transmission/disequilibrium test: history, subdivision, and admixture. Am J Hum Genet. 1995;57:455–464.Google ScholarPubMed
30.Cooper, DN, Smith, BA, Cooke, HJ, Niemann, S, Schmidtke, J. An estimate of unique DNA sequence heterozygosity in the human genome. Hum Genet. 1985;69:201–205.CrossRefGoogle ScholarPubMed
31.Nickerson, DA, Taylor, SL, Weiss, KM, et al.DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene [see comments]. Nat Genet. 1998;19:233–240.CrossRefGoogle Scholar
32.Wang, DG, Fan, JB, Siao, CJ, et al.Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998;280:1077–1082.CrossRefGoogle ScholarPubMed
33.Cargill, M. Characterization of single-nucleotide polymorphisms in coding regions of human genes (manuscript submitted).Google Scholar
34.Roychoudhury, AK, Nei, M. Human Polymorphic Genes World Distribution. New York, NY: Oxford University Press, Inc.;1988.Google Scholar
35.Orita, M, Iwahana, H, Kanazawa, H, Hayashi, K, Sekiya, T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA. 1989;86:2766–2770.CrossRefGoogle ScholarPubMed
36.Fischer, SG, Lerman, LS. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci USA. 1983;80:1579–1583.CrossRefGoogle ScholarPubMed
37.Oefner, PJ, Underbill, PA. Comparative DNA sequencing by denaturing high-performance liquid chromatography (DHPLC). Am J Hum Genet. 1995;57:A266.Google Scholar
38.Smith, J, Modrich, P. Mutation detection with MutH, MutL, and MutS mismatch repair proteins. Proc Natl Acad Sci USA. 1996;93:4374–4379.CrossRefGoogle ScholarPubMed
39.McGall, G, Labadie, J, Brock, P, Wallraff, G, Nguyen, T, Hinsberg, W. Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proc Natl Acad Sci USA. 1996;93:13555–13560.CrossRefGoogle ScholarPubMed
40.Chee, M, Yang, R, Hubbell, E, Berno, A, et al.Accessing genetic information with high-density DNA arrays. Science. 1996;274:610–614.CrossRefGoogle ScholarPubMed
41.Hacia, JG, Brody, LC, Chee, MS, Fodor, SP, Collins, FS. Detection of heterozygous mutations in BRCA1 using high-density oligonucleotide arrays and two-colour fluorescence analysis [see comments]. Nat Genet. 1996;14:441–447.CrossRefGoogle ScholarPubMed
42.Lieberman, JA, Koreen, AR. Neurochemistry and neuroendocrinology of schizophrenia: a selective review. Schizophr Bull. 1993;19:371–429.CrossRefGoogle ScholarPubMed
43.Ross, CA, Pearlson, GD. Schizophrenia, the heteromodal association neocortex and development: potential for a neurogenetic approach [see comments]. Trends Neurosci. 1996;19:171–176.CrossRefGoogle ScholarPubMed
44.McGuire, PK, Shah, GM, Murray, RM. Increased blood flow in Broca's area during auditory hallucinations in schizophrenia [see comments]. Lancet. 1993;342:703–706.CrossRefGoogle ScholarPubMed
45.Selemon, LD, Rajkowska, G, Goldman-Rakic, PS. Abnormally high neuronal density in the schizophrenic cortex. A morphometric analysis of prefrontal area 9 and occipital area 17. Arch Gen Psychiatry. 1995;52:805–818; discussion: 819–820.CrossRefGoogle ScholarPubMed
46.Akbarian, S, Bunney, WE Jr, Potkin, SG, et al.Altered distribution of nicotinamide-adenine dinucleotide phos-phate-diaphorase cells in frontal lobe of schizophrenics implies disturbances of cortical development. Arch Gen Psychiatry. 1993;50:169–177.CrossRefGoogle ScholarPubMed
47.Akbarian, S, Kim, JJ, Potkin, SG, Hetrick, WP, Bunney, WE Jr, Jones, EG. Maldistribution of interstitial neurons in prefrontal white matter of the brains of schizophrenic patients. Arch Gen Psychiatry. 1996;53:425–436.CrossRefGoogle ScholarPubMed
48.DeSilva, U, D'Arcangelo, G, Braden, VV, et al.The human reelin gene: isolation, sequencing, and mapping on chromosome 7 [letter]. Genome Res. 1997;7:157–164.CrossRefGoogle ScholarPubMed
49.Orioli, D, Klein, R. The Eph receptor family: axonal guidance by contact repulsion. Trends Genet. 1997;13:354–359.CrossRefGoogle ScholarPubMed
50.Bulfone, A, Puelles, L, Porteus, MH, et al.Spatially restricted expression of Dlx-1, Dlx-2 (Tes-1), Gbx-2, and Wnt- 3 in the embryonic day 12.5 mouse forebrain defines potential transverse and longitudinal segmental boundaries. J Neurosci. 1993;13:3155–3172.CrossRefGoogle ScholarPubMed
51.Murphy, DB, Wiese, S, Burfeind, P, et al.Human brain factor 1, a new member of the fork head gene family. Genomics. 1994;21:551–557.CrossRefGoogle ScholarPubMed
52.Oin, S, LaRosa, G, Campbell, JJ, et al.Expression of monocyte chemoattractant protein-1 and interleukin-8 receptors on subsets of T cells: correlation with transendothelial chemotactic potential. Eur J Immunol. 1996;26:640–647.Google Scholar
53.Swerdlow, NR, Geyer, MA. Using an animal model of deficient sensorimotor gating to study the pathophysiology and new treatments of schizophrenia. Schizophr Bull. 1998;24:285–301.CrossRefGoogle Scholar
54.Lesch, KP, Bengel, D, Heils, A, et al.Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region [see comments]. Science. 1996;274:1527–1531.CrossRefGoogle ScholarPubMed
55.Inayama, Y, Yoneda, H, Sakai, T, et al.Positive association between a DNA sequence variant in the serotonin 2A receptor gene and schizophrenia. Am J Med Genet. 1996;67:103–105.3.0.CO;2-S>CrossRefGoogle ScholarPubMed
56.Ebstein, RP, et al.Dopamine D4 receptor (D4DR) exon III polymorphism associated with the human personality trait of novelty seeking. Nat Genet. 1996;12:78–80.CrossRefGoogle ScholarPubMed
57.Gelernter, J, Van Dyck, C, van Kammen, DP, et al.Ciliary neurotrophic factor null allele frequencies in schizophrenia, affective disorders, and Alzheimer's disease. Am J Med Genet. 1997;74:497–500.3.0.CO;2-L>CrossRefGoogle ScholarPubMed
58.Spielman, RS, Ewens, WJ. A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet. 1998;62:450–458.CrossRefGoogle ScholarPubMed
59.Bertina, RM, van der Linden, IK, Engesser, L, Muller, HP, Brommer, EJ. Hereditary heparin cofactor II deficiency and the risk of development of thrombosis. Thromb Haemost. 1987;57:196–200.Google ScholarPubMed
60.Botstein, D, White, RL, Skolnick, M, Davis, RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32:314–331.Google ScholarPubMed
61.Livak, KJ, Flood, SJ, Marmaro, J, Giusti, W, Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 1995;4:357–362.CrossRefGoogle ScholarPubMed
62.Liu, Q, Thorland, EC, Heit, JA, Sommer, SS. Overlapping PCR for bidirectional PCR amplification of specific alleles: a rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes. Genome Res. 1997;7:389–398.CrossRefGoogle ScholarPubMed
63.Samiotaki, M, Kwiatkowski, M, Parik, J, Landegren, U. Dual-color detection of DNA sequence variants by lig-ase-mediated analysis. Genomics. 1994;20:238–242.CrossRefGoogle ScholarPubMed
64.Kobayashi, M, Rappaport, E, Blasband, A, et al.Fluorescence-based DNA minisequence analysis for detection of known single-base changes in genomic DNA. Mol Cell Probes. 1995;9:175–182.CrossRefGoogle ScholarPubMed
65.Syvanen, AC, Sajantila, A, Lukka, M. Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am J Hum Genet. 1993;52:46–59.Google ScholarPubMed
66.Pastinen, T, Partanen, J, Syvanen, AC. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin Chem. 1996;42:1391–1397.CrossRefGoogle ScholarPubMed
67.Shumaker, JM, Metspalu, A, Caskey, CT. Mutation detection by solid phase primer extension. Hum Mutat. 1996;7:346–354.3.0.CO;2-6>CrossRefGoogle ScholarPubMed
68.Chen, X, Zehnbauer, B, Gnirke, A, Kwok, PY. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc Natl Acad Sci USA. 1997;94:10756–10761.CrossRefGoogle ScholarPubMed